Sodium channels that are modified by the addition of batrachotoxin (BTX) differ in many ways from normal sodium channels. For example, the modified channels activate with first order kinetics and activate more slowly than do normal sodium channels. These results suggest that BTX slows down one of the conformational changes which occur during channel opening, and that this conformational change becomes rate-limiting. A theory was developed to calculate partition energies of all amino acid side chains as a function of the distance of the alpha-carbon from a water-protein, a water-lipid, and a protein-lipid interface. This theory was used to develop a program that predicts the manner in which amphipathic alpha-helices with specific sequences will stack side by side to form a tight protein barrier between water and an apolar lipid phase. The program, in turn, was used to predict molecular conformations for apolipoproteins and for several membrane channel proteins.